{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Larval\" and experiment.platform = \"BGISEQ\"", "rows": [[28093, "SRR26196850", "SRX21908248", "SRS18993956", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa mutant  clutch 4", "GSM7808262", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa mutant  clutch 4", "Standard processing by BGI.p HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM7808262", "GSM7808262: elipsa mutant  clutch 4; Danio rerio; RNA Seq", "GSM7808262 r1", "GSM7808262", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaMUT4_1.fq.gz ElipsaMUT4_2.fq.gz", "fastq fastq", 4536153000.0, 22680765.0, "GSM7808262 r1", "0:100 1:100", "A:1194964224;C:1059904764;G:1074108947;T:1207175065;N:0", 100, 100, null, null, 1194964224, 1059904764, 1074108947, 1207175065, 0, "SRX21908248", "SRS18993956", "SRA1721841", "NTNU", "NTNU", 2, 0.93991, 0.94735, 0.10392, 0.10318, 0.66434, 0.66344, 0.48911, 0.49311, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28094, "SRR26196851", "SRX21908247", "SRS18993955", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa mutant  clutch 3", "GSM7808261", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa mutant  clutch 3", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM7808261", "GSM7808261: elipsa mutant  clutch 3; Danio rerio; RNA Seq", "GSM7808261 r1", "GSM7808261", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaMUT3_1.fq.gz ElipsaMUT3_2.fq.gz", "fastq fastq", 4547581600.0, 22737908.0, "GSM7808261 r1", "0:100 1:100", "A:1183476304;C:1077021222;G:1092963681;T:1194120393;N:0", 100, 100, null, null, 1183476304, 1077021222, 1092963681, 1194120393, 0, "SRX21908247", "SRS18993955", "SRA1721841", "NTNU", "NTNU", 2, 0.95029, 0.95874, 0.09085, 0.09059, 0.66856, 0.66722, 0.48534, 0.48545, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28095, "SRR26196852", "SRX21908246", "SRS18993954", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa mutant  clutch 2", "GSM7808260", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa mutant  clutch 2", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM7808260", "GSM7808260: elipsa mutant  clutch 2; Danio rerio; RNA Seq", "GSM7808260 r1", "GSM7808260", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaMUT2_1.fq.gz ElipsaMUT2_2.fq.gz", "fastq fastq", 4544444600.0, 22722223.0, "GSM7808260 r1", "0:100 1:100", "A:1186329827;C:1072965608;G:1087757513;T:1197391652;N:0", 100, 100, null, null, 1186329827, 1072965608, 1087757513, 1197391652, 0, "SRX21908246", "SRS18993954", "SRA1721841", "NTNU", "NTNU", 2, 0.94545, 0.95403, 0.09705, 0.09653, 0.66576, 0.66466, 0.47893, 0.47882, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28096, "SRR26196853", "SRX21908245", "SRS18993953", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa mutant  clutch 1", "GSM7808259", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa mutant  clutch 1", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM7808259", "GSM7808259: elipsa mutant  clutch 1; Danio rerio; RNA Seq", "GSM7808259 r1", "GSM7808259", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaMUT1_1.fq.gz ElipsaMUT1_2.fq.gz", "fastq fastq", 4561346400.0, 22806732.0, "GSM7808259 r1", "0:100 1:100", "A:1192227498;C:1073309826;G:1091718946;T:1204090130;N:0", 100, 100, null, null, 1192227498, 1073309826, 1091718946, 1204090130, 0, "SRX21908245", "SRS18993953", "SRA1721841", "NTNU", "NTNU", 2, 0.94079, 0.94928, 0.09838, 0.09859, 0.67093, 0.66975, 0.47837, 0.4824, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28097, "SRR26196854", "SRX21908244", "SRS18993950", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa control  clutch 4", "GSM7808258", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa control  clutch 4", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM7808258", "GSM7808258: elipsa control  clutch 4; Danio rerio; RNA Seq", "GSM7808258 r1", "GSM7808258", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaCTRL4_1.fq.gz ElipsaCTRL4_2.fq.gz", "fastq fastq", 4534543600.0, 22672718.0, "GSM7808258 r1", "0:100 1:100", "A:1195456125;C:1060510332;G:1073683545;T:1204893598;N:0", 100, 100, null, null, 1195456125, 1060510332, 1073683545, 1204893598, 0, "SRX21908244", "SRS18993950", "SRA1721841", "NTNU", "NTNU", 2, 0.94686, 0.95523, 0.0948, 0.09459, 0.66259, 0.66093, 0.49251, 0.49154, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28098, "SRR26196855", "SRX21908243", "SRS18993952", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa control  clutch 3", "GSM7808257", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa control  clutch 3", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM7808257", "GSM7808257: elipsa control  clutch 3; Danio rerio; RNA Seq", "GSM7808257 r1", "GSM7808257", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaCTRL3_1.fq.gz ElipsaCTRL3_2.fq.gz", "fastq fastq", 4546464800.0, 22732324.0, "GSM7808257 r1", "0:100 1:100", "A:1192169234;C:1070218166;G:1081895902;T:1202181498;N:0", 100, 100, null, null, 1192169234, 1070218166, 1081895902, 1202181498, 0, "SRX21908243", "SRS18993952", "SRA1721841", "NTNU", "NTNU", 2, 0.94937, 0.95815, 0.09867, 0.09825, 0.66574, 0.66478, 0.49056, 0.48959, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28099, "SRR26196856", "SRX21908242", "SRS18993951", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa control  clutch 2", "GSM7808256", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa control  clutch 2", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM7808256", "GSM7808256: elipsa control  clutch 2; Danio rerio; RNA Seq", "GSM7808256 r1", "GSM7808256", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaCTRL2_1.fq.gz ElipsaCTRL2_2.fq.gz", "fastq fastq", 4557679200.0, 22788396.0, "GSM7808256 r1", "0:100 1:100", "A:1184954651;C:1080955864;G:1098377272;T:1193391413;N:0", 100, 100, null, null, 1184954651, 1080955864, 1098377272, 1193391413, 0, "SRX21908242", "SRS18993951", "SRA1721841", "NTNU", "NTNU", 2, 0.94378, 0.95076, 0.0855, 0.0847, 0.66604, 0.66342, 0.48858, 0.48404, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28100, "SRR26196857", "SRX21908241", "SRS18993949", "SRP463504", "PRJNA1021586", "Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish", "GSE244171", "Transcriptome Analysis", "Cilia are slender  hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system  primary cilia contribute to signaling and sensory perception  while motile cilia facilitate cerebrospinal fluid flow. Here  we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology  especially in the cerebellum  and lead to altered gene expression profiles. Using whole brain calcium imaging  we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish  our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression  we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:38868197", null, "elipsa control  clutch 1", "GSM7808255", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "elipsa control  clutch 1", "Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM7808255", "GSM7808255: elipsa control  clutch 1; Danio rerio; RNA Seq", "GSM7808255 r1", "GSM7808255", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP463504", null, null, "ElipsaCTRL1_1.fq.gz ElipsaCTRL1_2.fq.gz", "fastq fastq", 4566618600.0, 22833093.0, "GSM7808255 r1", "0:100 1:100", "A:1193092402;C:1076659586;G:1094193492;T:1202673120;N:0", 100, 100, null, null, 1193092402, 1076659586, 1094193492, 1202673120, 0, "SRX21908241", "SRS18993949", "SRA1721841", "NTNU", "NTNU", 2, 0.94269, 0.94899, 0.09816, 0.09712, 0.66991, 0.66925, 0.47671, 0.46995, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-09-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30075, "SRR27700027", "SRX23366859", "SRS20229171", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh mutant  clutch 4", "GSM8031712", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh mutant  clutch 4", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM8031712", "GSM8031712: Smh mutant  clutch 4; Danio rerio; RNA Seq", "GSM8031712 r1", "GSM8031712", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhMUT4_1.fq.gz SmhMUT4_2.fq.gz", "fastq fastq", 4550057400.0, 22750287.0, "GSM8031712 r1", "0:100 1:100", "A:1198976754;C:1064190197;G:1077491671;T:1209398778;N:0", 100, 100, null, null, 1198976754, 1064190197, 1077491671, 1209398778, 0, "SRX23366859", "SRS20229171", "SRA1790727", "NTNU", "NTNU", 2, 0.94285, 0.95266, 0.101, 0.10096, 0.66145, 0.65989, 0.48209, 0.47768, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30076, "SRR27700028", "SRX23366858", "SRS20229175", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh mutant  clutch 3", "GSM8031711", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh mutant  clutch 3", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM8031711", "GSM8031711: Smh mutant  clutch 3; Danio rerio; RNA Seq", "GSM8031711 r1", "GSM8031711", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhMUT3_1.fq.gz SmhMUT3_2.fq.gz", "fastq fastq", 4545452600.0, 22727263.0, "GSM8031711 r1", "0:100 1:100", "A:1188958937;C:1071903723;G:1087032258;T:1197557682;N:0", 100, 100, null, null, 1188958937, 1071903723, 1087032258, 1197557682, 0, "SRX23366858", "SRS20229175", "SRA1790727", "NTNU", "NTNU", 2, 0.94501, 0.95409, 0.09005, 0.08947, 0.66149, 0.66062, 0.46824, 0.48019, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30077, "SRR27700029", "SRX23366857", "SRS20229173", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh mutant  clutch 2", "GSM8031710", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh mutant  clutch 2", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM8031710", "GSM8031710: Smh mutant  clutch 2; Danio rerio; RNA Seq", "GSM8031710 r1", "GSM8031710", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhMUT2_1.fq.gz SmhMUT2_2.fq.gz", "fastq fastq", 4548042000.0, 22740210.0, "GSM8031710 r1", "0:100 1:100", "A:1184618587;C:1077947166;G:1089628929;T:1195847318;N:0", 100, 100, null, null, 1184618587, 1077947166, 1089628929, 1195847318, 0, "SRX23366857", "SRS20229173", "SRA1790727", "NTNU", "NTNU", 2, 0.94502, 0.95416, 0.09209, 0.092, 0.66407, 0.66214, 0.48538, 0.48509, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30078, "SRR27700030", "SRX23366856", "SRS20229174", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh mutant  clutch 1", "GSM8031709", null, "source name:whole larvae|tissue:whole larvae|genotype: / |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh mutant  clutch 1", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype: / |treatment:no treatment", "GSM8031709", "GSM8031709: Smh mutant  clutch 1; Danio rerio; RNA Seq", "GSM8031709 r1", "GSM8031709", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhMUT1_1.fq.gz SmhMUT1_2.fq.gz", "fastq fastq", 4544759600.0, 22723798.0, "GSM8031709 r1", "0:100 1:100", "A:1194011331;C:1066502346;G:1077923006;T:1206322917;N:0", 100, 100, null, null, 1194011331, 1066502346, 1077923006, 1206322917, 0, "SRX23366856", "SRS20229174", "SRA1790727", "NTNU", "NTNU", 2, 0.945, 0.95433, 0.09733, 0.09796, 0.66034, 0.65951, 0.477, 0.47705, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30079, "SRR27700031", "SRX23366855", "SRS20229172", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh control  clutch 4", "GSM8031708", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh control  clutch 4", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM8031708", "GSM8031708: Smh control  clutch 4; Danio rerio; RNA Seq", "GSM8031708 r1", "GSM8031708", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhCTRL4_1.fq.gz SmhCTRL4_2.fq.gz", "fastq fastq", 4536141000.0, 22680705.0, "GSM8031708 r1", "0:100 1:100", "A:1196842043;C:1059535727;G:1071488375;T:1208274855;N:0", 100, 100, null, null, 1196842043, 1059535727, 1071488375, 1208274855, 0, "SRX23366855", "SRS20229172", "SRA1790727", "NTNU", "NTNU", 2, 0.94102, 0.95093, 0.09453, 0.09431, 0.66403, 0.6631, 0.49804, 0.49818, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30080, "SRR27700032", "SRX23366854", "SRS20229170", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh control  clutch 3", "GSM8031707", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh control  clutch 3", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM8031707", "GSM8031707: Smh control  clutch 3; Danio rerio; RNA Seq", "GSM8031707 r1", "GSM8031707", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhCTRL3_1.fq.gz SmhCTRL3_2.fq.gz", "fastq fastq", 4543416000.0, 22717080.0, "GSM8031707 r1", "0:100 1:100", "A:1189755812;C:1071666785;G:1082665579;T:1199327824;N:0", 100, 100, null, null, 1189755812, 1071666785, 1082665579, 1199327824, 0, "SRX23366854", "SRS20229170", "SRA1790727", "NTNU", "NTNU", 2, 0.94571, 0.95506, 0.08989, 0.09005, 0.6632, 0.66107, 0.49631, 0.49649, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30081, "SRR27700033", "SRX23366853", "SRS20229169", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh control  clutch 2", "GSM8031706", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh control  clutch 2", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM8031706", "GSM8031706: Smh control  clutch 2; Danio rerio; RNA Seq", "GSM8031706 r1", "GSM8031706", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhCTRL2_2.fq.gz SmhCTRL2_1.fq.gz", "fastq fastq", 4536576000.0, 22682880.0, "GSM8031706 r1", "0:100 1:100", "A:1180961957;C:1074391564;G:1088552770;T:1192669709;N:0", 100, 100, null, null, 1180961957, 1074391564, 1088552770, 1192669709, 0, "SRX23366853", "SRS20229169", "SRA1790727", "NTNU", "NTNU", 2, 0.94324, 0.95313, 0.08618, 0.08685, 0.66399, 0.66216, 0.49362, 0.49644, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [30082, "SRR27700034", "SRX23366852", "SRS20229168", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh control  clutch 1", "GSM8031705", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh control  clutch 1", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM8031705", "GSM8031705: Smh control  clutch 1; Danio rerio; RNA Seq", "GSM8031705 r1", "GSM8031705", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhCTRL1_1.fq.gz SmhCTRL1_2.fq.gz", "fastq fastq", 4546026800.0, 22730134.0, "GSM8031705 r1", "0:100 1:100", "A:1201447089;C:1060722844;G:1073012718;T:1210844149;N:0", 100, 100, null, null, 1201447089, 1060722844, 1073012718, 1210844149, 0, "SRX23366852", "SRS20229168", "SRA1790727", "NTNU", "NTNU", 2, 0.94554, 0.95419, 0.09192, 0.09168, 0.66436, 0.66222, 0.4762, 0.48114, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [31825, "SRR28700412", "SRX24268115", "SRS21034395", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "PN 2", null, "isolate:PN2|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "PN 2", "PN 2", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "PN_2_1.fq.gz PN_2_2.fq.gz", "fastq fastq", 6385048200.0, 21283494.0, "PN 2 1.fq.gz", "0:150 1:150", "A:1722127999;C:1463645587;G:1483173818;T:1716100796;N:0", 150, 150, null, null, 1722127999, 1463645587, 1483173818, 1716100796, 0, "SRX24268115", "SRS21034395", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31826, "SRR28700413", "SRX24268114", "SRS21034397", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "PN 1", null, "isolate:PN1|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "PN 1", "PN 1", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "PN_1_1.fq.gz PN_1_2.fq.gz", "fastq fastq", 6692894100.0, 22309647.0, "PN 1 1.fq.gz", "0:150 1:150", "A:1827107021;C:1513034624;G:1533077624;T:1819674831;N:0", 150, 150, null, null, 1827107021, 1513034624, 1533077624, 1819674831, 0, "SRX24268114", "SRS21034397", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31827, "SRR28700414", "SRX24268113", "SRS21034396", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "EC 4", null, "isolate:EC4|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "EC 4", "EC 4", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "EC_4_1.fq.gz EC_4_2.fq.gz", "fastq fastq", 6688857000.0, 22296190.0, "EC 4 1.fq.gz", "0:150 1:150", "A:1820989545;C:1516814697;G:1537970654;T:1813082104;N:0", 150, 150, null, null, 1820989545, 1516814697, 1537970654, 1813082104, 0, "SRX24268113", "SRS21034396", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31828, "SRR28700415", "SRX24268112", "SRS21034392", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "EC 3", null, "isolate:EC3|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "EC 3", "EC 3", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "EC_3_1.fq.gz EC_3_2.fq.gz", "fastq fastq", 6696553800.0, 22321846.0, "EC 3 1.fq.gz", "0:150 1:150", "A:1821249100;C:1520587242;G:1541238550;T:1813478908;N:0", 150, 150, null, null, 1821249100, 1520587242, 1541238550, 1813478908, 0, "SRX24268112", "SRS21034392", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31829, "SRR28700416", "SRX24268111", "SRS21034391", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "EC 2", null, "isolate:EC2|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "EC 2", "EC 2", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "EC_2_1.fq.gz EC_2_2.fq.gz", "fastq fastq", 6702179400.0, 22340598.0, "EC 2 1.fq.gz", "0:150 1:150", "A:1816692261;C:1527379142;G:1547365810;T:1810742187;N:0", 150, 150, null, null, 1816692261, 1527379142, 1547365810, 1810742187, 0, "SRX24268111", "SRS21034391", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31830, "SRR28700417", "SRX24268110", "SRS21034390", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "EC 1", null, "isolate:EC1|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "EC 1", "EC 1", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "EC_1_1.fq.gz EC_1_2.fq.gz", "fastq fastq", 6686053500.0, 22286845.0, "EC 1 1.fq.gz", "0:150 1:150", "A:1812022780;C:1524359858;G:1544847441;T:1804823421;N:0", 150, 150, null, null, 1812022780, 1524359858, 1544847441, 1804823421, 0, "SRX24268110", "SRS21034390", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31831, "SRR28700418", "SRX24268109", "SRS21034388", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "Control 4", null, "isolate:con4|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "Control 4", "Control 4", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "Control_4_1.fq.gz Control_4_2.fq.gz", "fastq fastq", 6669700500.0, 22232335.0, "Control 4 1.fq.gz", "0:150 1:150", "A:1804178265;C:1523547469;G:1543839484;T:1798135282;N:0", 150, 150, null, null, 1804178265, 1523547469, 1543839484, 1798135282, 0, "SRX24268109", "SRS21034388", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31832, "SRR28700419", "SRX24268108", "SRS21034387", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "Control 3", null, "isolate:con3|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "Control 3", "Control 3", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "Control_3_1.fq.gz Control_3_2.fq.gz", "fastq fastq", 6683518800.0, 22278396.0, "Control 3 1.fq.gz", "0:150 1:150", "A:1808495506;C:1525725204;G:1545930043;T:1803368047;N:0", 150, 150, null, null, 1808495506, 1525725204, 1545930043, 1803368047, 0, "SRX24268108", "SRS21034387", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31833, "SRR28700420", "SRX24268107", "SRS21034386", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "PN 4", null, "isolate:PN4|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "PN 4", "PN 4", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "PN_4_1.fq.gz PN_4_2.fq.gz", "fastq fastq", 6649316100.0, 22164387.0, "PN 4 1.fq.gz", "0:150 1:150", "A:1809816121;C:1508072480;G:1528272654;T:1803154845;N:0", 150, 150, null, null, 1809816121, 1508072480, 1528272654, 1803154845, 0, "SRX24268107", "SRS21034386", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31834, "SRR28700421", "SRX24268106", "SRS21034389", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "PN 3", null, "isolate:PN3|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "PN 3", "PN 3", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "PN_3_1.fq.gz PN_3_2.fq.gz", "fastq fastq", 6616113900.0, 22053713.0, "PN 3 1.fq.gz", "0:150 1:150", "A:1802283686;C:1499008018;G:1519150002;T:1795672194;N:0", 150, 150, null, null, 1802283686, 1499008018, 1519150002, 1795672194, 0, "SRX24268106", "SRS21034389", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31835, "SRR28700422", "SRX24268105", "SRS21034385", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "Control 2", null, "isolate:con2|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "Control 2", "Control 2", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "Control_2_1.fq.gz Control_2_2.fq.gz", "fastq fastq", 6701719200.0, 22339064.0, "Control 2 1.fq.gz", "0:150 1:150", "A:1812352260;C:1531672703;G:1551377072;T:1806317165;N:0", 150, 150, null, null, 1812352260, 1531672703, 1551377072, 1806317165, 0, "SRX24268105", "SRS21034385", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [31836, "SRR28700423", "SRX24268104", "SRS21034384", "SRP501894", "PRJNA1100624", "Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis", "PRJNA1100624", "Other", "Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.", null, null, null, null, "Control 1", null, "isolate:con1|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish", "Control 1", "Control 1", "Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP501894", null, null, "Control_1_1.fq.gz Control_1_2.fq.gz", "fastq fastq", 6720214500.0, 22400715.0, "Control 1 1.fq.gz", "0:150 1:150", "A:1814883015;C:1537948710;G:1559376116;T:1808006659;N:0", 150, 150, null, null, 1814883015, 1537948710, 1559376116, 1808006659, 0, "SRX24268104", "SRS21034384", null, null, "Xiangyang No.1 People's Hospital, Hubei University of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-15", "Larval", "Larval", "Undetermined", "Undetermined"], [34182, "SRR31399561", "SRX26768859", "SRS23256160", "SRP546207", "PRJNA1188114", "Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome", "GSE282310", "Transcriptome Analysis", "Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8\u20139 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.", null, null, null, "eif6 3", "GSM8641203", null, "source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO|geo loc name:missing|collection date:missing", "eif6 3", "Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3\u2019 adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3\u2019 adapter sequence  2 were 5\u2019 3\u2019 adapter ligation products  3 were 5\u2019 5\u2019 adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values", "whole larvae", "5 dpf", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO", "GSM8641203", "GSM8641203: eif6 3; Danio rerio; RNA Seq", "GSM8641203 r1", "GSM8641203", "1", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP546207", null, null, "eif6_3_1.fq.gz eif6_3_2.fq.gz", "fastq fastq", 6955801200.0, 34779006.0, "GSM8641203 r1", "0:100 1:100", "A:1784502248;C:1653592398;G:1716091635;T:1801614919;N:0", 100, 100, null, null, 1784502248, 1653592398, 1716091635, 1801614919, 0, "SRX26768859", "SRS23256160", "SRA2017777", "Cleveland Clinic", "Cleveland Clinic", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-11-19", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [34183, "SRR31399562", "SRX26768858", "SRS23256161", "SRP546207", "PRJNA1188114", "Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome", "GSE282310", "Transcriptome Analysis", "Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8\u20139 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.", null, null, null, "eif6 2", "GSM8641202", null, "source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO|geo loc name:missing|collection date:missing", "eif6 2", "Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3\u2019 adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3\u2019 adapter sequence  2 were 5\u2019 3\u2019 adapter ligation products  3 were 5\u2019 5\u2019 adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values", "whole larvae", "5 dpf", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO", "GSM8641202", "GSM8641202: eif6 2; Danio rerio; RNA Seq", "GSM8641202 r1", "GSM8641202", "1", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP546207", null, null, "eif6_2_1.fq.gz eif6_2_2.fq.gz", "fastq fastq", 6968721400.0, 34843607.0, "GSM8641202 r1", "0:100 1:100", "A:1798630009;C:1650901437;G:1708195694;T:1810994260;N:0", 100, 100, null, null, 1798630009, 1650901437, 1708195694, 1810994260, 0, "SRX26768858", "SRS23256161", "SRA2017777", "Cleveland Clinic", "Cleveland Clinic", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-11-19", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [34184, "SRR31399563", "SRX26768857", "SRS23256159", "SRP546207", "PRJNA1188114", "Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome", "GSE282310", "Transcriptome Analysis", "Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8\u20139 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.", null, null, null, "eif6 1", "GSM8641201", null, "source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO|geo loc name:missing|collection date:missing", "eif6 1", "Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3\u2019 adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3\u2019 adapter sequence  2 were 5\u2019 3\u2019 adapter ligation products  3 were 5\u2019 5\u2019 adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values", "whole larvae", "5 dpf", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "tissue:whole larvae|cell line:5 dpf|genotype:eif6 KO", "GSM8641201", "GSM8641201: eif6 1; Danio rerio; RNA Seq", "GSM8641201 r1", "GSM8641201", "1", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP546207", null, null, "eif6_1_1.fq.gz eif6_1_2.fq.gz", "fastq fastq", 6976474200.0, 34882371.0, "GSM8641201 r1", "0:100 1:100", "A:1819387431;C:1630709320;G:1698463303;T:1827914146;N:0", 100, 100, null, null, 1819387431, 1630709320, 1698463303, 1827914146, 0, "SRX26768857", "SRS23256159", "SRA2017777", "Cleveland Clinic", "Cleveland Clinic", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-11-19", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [34185, "SRR31399564", "SRX26768856", "SRS23256158", "SRP546207", "PRJNA1188114", "Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome", "GSE282310", "Transcriptome Analysis", "Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8\u20139 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.", null, null, null, "wt3", "GSM8641200", null, "source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype|geo loc name:missing|collection date:missing", "wt3", "Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3\u2019 adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3\u2019 adapter sequence  2 were 5\u2019 3\u2019 adapter ligation products  3 were 5\u2019 5\u2019 adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values", "whole larvae", "5 dpf", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype", "GSM8641200", "GSM8641200: wt3; Danio rerio; RNA Seq", "GSM8641200 r1", "GSM8641200", "1", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP546207", null, null, "wt3_1.fq.gz wt3_2.fq.gz", "fastq fastq", 6990771600.0, 34953858.0, "GSM8641200 r1", "0:100 1:100", "A:1823561732;C:1639273273;G:1691098287;T:1836838308;N:0", 100, 100, null, null, 1823561732, 1639273273, 1691098287, 1836838308, 0, "SRX26768856", "SRS23256158", "SRA2017777", "Cleveland Clinic", "Cleveland Clinic", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-11-19", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [34186, "SRR31399565", "SRX26768855", "SRS23256157", "SRP546207", "PRJNA1188114", "Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome", "GSE282310", "Transcriptome Analysis", "Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8\u20139 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.", null, null, null, "wt2", "GSM8641199", null, "source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype|geo loc name:missing|collection date:missing", "wt2", "Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3\u2019 adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3\u2019 adapter sequence  2 were 5\u2019 3\u2019 adapter ligation products  3 were 5\u2019 5\u2019 adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values", "whole larvae", "5 dpf", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype", "GSM8641199", "GSM8641199: wt2; Danio rerio; RNA Seq", "GSM8641199 r1", "GSM8641199", "1", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP546207", null, null, "wt2_1.fq.gz wt2_2.fq.gz", "fastq fastq", 6996780600.0, 34983903.0, "GSM8641199 r1", "0:100 1:100", "A:1819793027;C:1646550105;G:1701161650;T:1829275818;N:0", 100, 100, null, null, 1819793027, 1646550105, 1701161650, 1829275818, 0, "SRX26768855", "SRS23256157", "SRA2017777", "Cleveland Clinic", "Cleveland Clinic", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-11-19", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [34187, "SRR31399566", "SRX26768854", "SRS23256156", "SRP546207", "PRJNA1188114", "Reduced  EIF6 dosage attenuates TP53 activation in models  of Shwachman Diamond syndrome", "GSE282310", "Transcriptome Analysis", "Shwachman Diamond syndrome SDS is characterized by neutropenia  exocrine pancreatic insufficiency  and bony abnormalities with an increased risk of myeloid neoplasia.  Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects.  We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models  confirmed in patient derived tissues  and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this  we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression  5 25% of the wildtype levels  that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS  EIF6  TP53  and cellular stress responses offer promising insights into SDS pathogenesis  somatic genetic rescue  and therapeutic strategies. Overall design: RNA was extracted from pools of 8\u20139 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 /  or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent  and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 /  and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39  we used EBSeq R package for differentially expressed gene detection between eif6 /  and eif6+/+ fold change > 2  and P < 0.05.", null, null, null, "wt1", "GSM8641198", null, "source name:whole larvae|tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype|geo loc name:missing|collection date:missing", "wt1", "Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly  reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3\u2019 adapter sequences were then trimmed from the remaining high quality reads. Finally  reads were removed if they: 1 lacked a 3\u2019 adapter sequence  2 were 5\u2019 3\u2019 adapter ligation products  3 were 5\u2019 5\u2019 adapter ligation products  4 were shorter than 18 nt  or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters:  f  N 0  M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values", "whole larvae", "5 dpf", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "tissue:whole larvae|cell line:5 dpf|genotype:eif6 wildtype", "GSM8641198", "GSM8641198: wt1; Danio rerio; RNA Seq", "GSM8641198 r1", "GSM8641198", "1", "RNA was harvested using TRIzol  following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP546207", null, null, "wt1_1.fq.gz wt1_2.fq.gz", "fastq fastq", 6976844600.0, 34884223.0, "GSM8641198 r1", "0:100 1:100", "A:1807619362;C:1649374675;G:1693243894;T:1826606669;N:0", 100, 100, null, null, 1807619362, 1649374675, 1693243894, 1826606669, 0, "SRX26768854", "SRS23256156", "SRA2017777", "Cleveland Clinic", "Cleveland Clinic", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-11-19", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [35980, "SRR33796117", "SRX29017800", "SRS25233880", "SRP589371", "PRJNA1256770", "Danio rerio Raw sequence reads", "PRJNA1256770", "Whole Genome Sequencing", "Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.", null, null, null, "Model organism or animal sample from Danio rerio", "Zebrafish treatment with polysaccharides", null, "strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: embryo whole body", "P2000 1", "P2000 1", "Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First  and second strand cDNA synthesis was performed  followed by end repair  A tailing  and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_randomPriming", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP589371", null, null, "P2000_1_1.fq.gz P2000_1_2.fq.gz", "fastq fastq", 6682157100.0, 22273857.0, "P2000 1 1.fq.gz", "0:150 1:150", "A:1750970707;C:1591819991;G:1593263349;T:1746103053;N:0", 150, 150, null, null, 1750970707, 1591819991, 1593263349, 1746103053, 0, "SRX29017800", "SRS25233880", "SRA2141272", "West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine", "West Anhui Universiaty", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-06-02", "Larval", "Larval", "Trunk", "Surface Structure"], [35981, "SRR33796118", "SRX29017799", "SRS25233880", "SRP589371", "PRJNA1256770", "Danio rerio Raw sequence reads", "PRJNA1256770", "Whole Genome Sequencing", "Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.", null, null, null, "Model organism or animal sample from Danio rerio", "Zebrafish treatment with polysaccharides", null, "strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: embryo whole body", "P1000 3", "P1000 3", "Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First  and second strand cDNA synthesis was performed  followed by end repair  A tailing  and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_randomPriming", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP589371", null, null, "P1000_3_1.fq.gz P1000_3_2.fq.gz", "fastq fastq", 6596943000.0, 21989810.0, "P1000 3 1.fq.gz", "0:150 1:150", "A:1725528987;C:1574140428;G:1576046656;T:1721226929;N:0", 150, 150, null, null, 1725528987, 1574140428, 1576046656, 1721226929, 0, "SRX29017799", "SRS25233880", "SRA2141272", "West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine", "West Anhui Universiaty", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-06-02", "Larval", "Larval", "Trunk", "Surface Structure"], [35982, "SRR33796119", "SRX29017798", "SRS25233880", "SRP589371", "PRJNA1256770", "Danio rerio Raw sequence reads", "PRJNA1256770", "Whole Genome Sequencing", "Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.", null, null, null, "Model organism or animal sample from Danio rerio", "Zebrafish treatment with polysaccharides", null, "strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: embryo whole body", "P1000 2", "P1000 2", "Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First  and second strand cDNA synthesis was performed  followed by end repair  A tailing  and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_randomPriming", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP589371", null, null, "P1000_2_1.fq.gz P1000_2_2.fq.gz", "fastq fastq", 6677331000.0, 22257770.0, "P1000 2 1.fq.gz", "0:150 1:150", "A:1758237128;C:1582217484;G:1584403835;T:1752472553;N:0", 150, 150, null, null, 1758237128, 1582217484, 1584403835, 1752472553, 0, "SRX29017798", "SRS25233880", "SRA2141272", "West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine", "West Anhui Universiaty", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-06-02", "Larval", "Larval", "Trunk", "Surface Structure"], [35983, "SRR33796120", "SRX29017797", "SRS25233880", "SRP589371", "PRJNA1256770", "Danio rerio Raw sequence reads", "PRJNA1256770", "Whole Genome Sequencing", "Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.", null, null, null, "Model organism or animal sample from Danio rerio", "Zebrafish treatment with polysaccharides", null, "strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: embryo whole body", "P1000 1", "P1000 1", "Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First  and second strand cDNA synthesis was performed  followed by end repair  A tailing  and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_randomPriming", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP589371", null, null, "P1000_1_1.fq.gz P1000_1_2.fq.gz", "fastq fastq", 6771926100.0, 22573087.0, "P1000 1 1.fq.gz", "0:150 1:150", "A:1788071352;C:1600799117;G:1602227700;T:1780827931;N:0", 150, 150, null, null, 1788071352, 1600799117, 1602227700, 1780827931, 0, "SRX29017797", "SRS25233880", "SRA2141272", "West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine", "West Anhui Universiaty", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-06-02", "Larval", "Larval", "Trunk", "Surface Structure"], [35984, "SRR33796121", "SRX29017796", "SRS25233880", "SRP589371", "PRJNA1256770", "Danio rerio Raw sequence reads", "PRJNA1256770", "Whole Genome Sequencing", "Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.", null, null, null, "Model organism or animal sample from Danio rerio", "Zebrafish treatment with polysaccharides", null, "strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: embryo whole body", "P500 3", "P500 3", "Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First  and second strand cDNA synthesis was performed  followed by end repair  A tailing  and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_randomPriming", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP589371", null, null, "P500_3_1.fq.gz P500_3_2.fq.gz", "fastq fastq", 6691956300.0, 22306521.0, "P500 3 1.fq.gz", "0:150 1:150", "A:1763763611;C:1584417511;G:1585842124;T:1757933054;N:0", 150, 150, null, null, 1763763611, 1584417511, 1585842124, 1757933054, 0, "SRX29017796", "SRS25233880", "SRA2141272", "West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine", "West Anhui Universiaty", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-06-02", "Larval", "Larval", "Trunk", "Surface Structure"], [35985, "SRR33796122", "SRX29017795", "SRS25233880", "SRP589371", "PRJNA1256770", "Danio rerio Raw sequence reads", "PRJNA1256770", "Whole Genome Sequencing", "Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.", null, null, null, "Model organism or animal sample from Danio rerio", "Zebrafish treatment with polysaccharides", null, "strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: embryo whole body", "P500 2", "P500 2", "Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First  and second strand cDNA synthesis was performed  followed by end repair  A tailing  and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_randomPriming", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP589371", null, null, "P500_2_1.fq.gz P500_2_2.fq.gz", "fastq fastq", 6720858300.0, 22402861.0, "P500 2 1.fq.gz", "0:150 1:150", "A:1752279513;C:1609781801;G:1611483135;T:1747313851;N:0", 150, 150, null, null, 1752279513, 1609781801, 1611483135, 1747313851, 0, "SRX29017795", "SRS25233880", "SRA2141272", "West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine", "West Anhui Universiaty", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-06-02", "Larval", "Larval", "Trunk", "Surface Structure"], [35986, "SRR33796123", "SRX29017794", "SRS25233880", "SRP589371", "PRJNA1256770", "Danio rerio Raw sequence reads", "PRJNA1256770", "Whole Genome Sequencing", "Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.", null, null, null, "Model organism or animal sample from Danio rerio", "Zebrafish treatment with polysaccharides", null, "strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: embryo whole body", "P500 1", "P500 1", "Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First  and second strand cDNA synthesis was performed  followed by end repair  A tailing  and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_randomPriming", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP589371", null, null, "P500_1_1.fq.gz P500_1_2.fq.gz", "fastq fastq", 6820862100.0, 22736207.0, "P500 1 1.fq.gz", "0:150 1:150", "A:1812260874;C:1601860387;G:1602603805;T:1804137034;N:0", 150, 150, null, null, 1812260874, 1601860387, 1602603805, 1804137034, 0, "SRX29017794", "SRS25233880", "SRA2141272", "West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine", "West Anhui Universiaty", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-06-02", "Larval", "Larval", "Trunk", "Surface Structure"], [35987, "SRR33796124", "SRX29017793", "SRS25233880", "SRP589371", "PRJNA1256770", "Danio rerio Raw sequence reads", "PRJNA1256770", "Whole Genome Sequencing", "Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.", null, null, null, "Model organism or animal sample from Danio rerio", "Zebrafish treatment with polysaccharides", null, "strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: embryo whole body", "MX 3", "MX 3", "Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First  and second strand cDNA synthesis was performed  followed by end repair  A tailing  and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_randomPriming", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP589371", null, null, "MX_3_1.fq.gz MX_3_2.fq.gz", "fastq fastq", 6795327600.0, 22651092.0, "MX 3 1.fq.gz", "0:150 1:150", "A:1768016462;C:1630727253;G:1632326554;T:1764257331;N:0", 150, 150, null, null, 1768016462, 1630727253, 1632326554, 1764257331, 0, "SRX29017793", "SRS25233880", "SRA2141272", "West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine", "West Anhui Universiaty", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-06-02", "Larval", "Larval", "Trunk", "Surface Structure"], [35988, "SRR33796125", "SRX29017792", "SRS25233880", "SRP589371", "PRJNA1256770", "Danio rerio Raw sequence reads", "PRJNA1256770", "Whole Genome Sequencing", "Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.", null, null, null, "Model organism or animal sample from Danio rerio", "Zebrafish treatment with polysaccharides", null, "strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: embryo whole body", "P2000 3", "P2000 3", "Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First  and second strand cDNA synthesis was performed  followed by end repair  A tailing  and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_randomPriming", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP589371", null, null, "P2000_3_1.fq.gz P2000_3_2.fq.gz", "fastq fastq", 6620786400.0, 22069288.0, "P2000 3 1.fq.gz", "0:150 1:150", "A:1736628496;C:1574653543;G:1577791512;T:1731712849;N:0", 150, 150, null, null, 1736628496, 1574653543, 1577791512, 1731712849, 0, "SRX29017792", "SRS25233880", "SRA2141272", "West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine", "West Anhui Universiaty", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-06-02", "Larval", "Larval", "Trunk", "Surface Structure"], [35989, "SRR33796126", "SRX29017791", "SRS25233880", "SRP589371", "PRJNA1256770", "Danio rerio Raw sequence reads", "PRJNA1256770", "Whole Genome Sequencing", "Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.", null, null, null, "Model organism or animal sample from Danio rerio", "Zebrafish treatment with polysaccharides", null, "strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: embryo whole body", "P2000 2", "P2000 2", "Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First  and second strand cDNA synthesis was performed  followed by end repair  A tailing  and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_randomPriming", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP589371", null, null, "P2000_2_1.fq.gz P2000_2_2.fq.gz", "fastq fastq", 6613914000.0, 22046380.0, "P2000 2 1.fq.gz", "0:150 1:150", "A:1733574880;C:1575483348;G:1576793005;T:1728062767;N:0", 150, 150, null, null, 1733574880, 1575483348, 1576793005, 1728062767, 0, "SRX29017791", "SRS25233880", "SRA2141272", "West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine", "West Anhui Universiaty", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-06-02", "Larval", "Larval", "Trunk", "Surface Structure"], [35990, "SRR33796127", "SRX29017790", "SRS25233880", "SRP589371", "PRJNA1256770", "Danio rerio Raw sequence reads", "PRJNA1256770", "Whole Genome Sequencing", "Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.", null, null, null, "Model organism or animal sample from Danio rerio", "Zebrafish treatment with polysaccharides", null, "strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: embryo whole body", "MX 2", "MX 2", "Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First  and second strand cDNA synthesis was performed  followed by end repair  A tailing  and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_randomPriming", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP589371", null, null, "MX_2_1.fq.gz MX_2_2.fq.gz", "fastq fastq", 6769929300.0, 22566431.0, "MX 2 1.fq.gz", "0:150 1:150", "A:1773923783;C:1611785261;G:1615111695;T:1769108561;N:0", 150, 150, null, null, 1773923783, 1611785261, 1615111695, 1769108561, 0, "SRX29017790", "SRS25233880", "SRA2141272", "West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine", "West Anhui Universiaty", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-06-02", "Larval", "Larval", "Trunk", "Surface Structure"], [35991, "SRR33796128", "SRX29017789", "SRS25233880", "SRP589371", "PRJNA1256770", "Danio rerio Raw sequence reads", "PRJNA1256770", "Whole Genome Sequencing", "Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.", null, null, null, "Model organism or animal sample from Danio rerio", "Zebrafish treatment with polysaccharides", null, "strain:transgenic neutrophil green fluorescent MPX|age:3 dpf|dev stage:embryo|collection date:2024 05 01|geo loc name:China: Zhejiang|sex:pooled male and female|tissue:whole body|disease:Immunosuppression|MX:control sample|P500:immune suppression model treated with 500 ug/mL polysaccharide|P1000:immune suppression model treated with 1000 ug/mL polysaccharide|P2000:immune suppression model treated with 2000 ug/mL polysaccharide|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: embryo whole body", "MX 1", "MX 1", "Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First  and second strand cDNA synthesis was performed  followed by end repair  A tailing  and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_randomPriming", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP589371", null, null, "MX_1_1.fq.gz MX_1_2.fq.gz", "fastq fastq", 6715295400.0, 22384318.0, "MX 1 1.fq.gz", "0:150 1:150", "A:1774590051;C:1584963102;G:1587348964;T:1768393283;N:0", 150, 150, null, null, 1774590051, 1584963102, 1587348964, 1768393283, 0, "SRX29017789", "SRS25233880", "SRA2141272", "West Anhui Universiaty|College of Biotechnology and Pharmaceutical Engine", "West Anhui Universiaty", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-06-02", "Larval", "Larval", "Trunk", "Surface Structure"], [52210, "SRR9021058", "SRX5799154", "SRS4730324", "SRP195685", "PRJNA541367", "Global 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The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_1_2_2.fq.gz BPS_1_2_1.fq.gz", "fastq fastq", 6959685000.0, 69596850.0, "BPS 1 2 1.fq.gz", "0:100 1:100", "A:1914426129;C:1574998719;G:1542052351;T:1927550147;N:657654", 100, 100, null, null, 1914426129, 1574998719, 1542052351, 1927550147, 657654, "SRX7351698", "SRS5811180", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94034, null, 0.14574, null, 0.69934, null, 0.47033, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55661, "SRR10674416", "SRX7351697", "SRS5811183", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. 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The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_1_1_1.fq.gz BPS_1_1_2.fq.gz", "fastq fastq", 7040826400.0, 70408264.0, "BPS 1 1 1.fq.gz", "0:100 1:100", "A:1915125100;C:1612334047;G:1578924466;T:1933922418;N:520369", 100, 100, null, null, 1915125100, 1612334047, 1578924466, 1933922418, 520369, "SRX7351697", "SRS5811183", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94114, null, 0.13158, null, 0.68903, null, 0.47739, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55662, "SRR10674417", "SRX7351696", "SRS5811179", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. 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The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "BPS_0_1_3_1.fq.gz BPS_0_1_3_2.fq.gz", "fastq fastq", 6992676800.0, 69926768.0, "BPS 0 1 3 1.fq.gz", "0:100 1:100", "A:1860627581;C:1643489002;G:1610508221;T:1877536968;N:515028", 100, 100, null, null, 1860627581, 1643489002, 1610508221, 1877536968, 515028, "SRX7351696", "SRS5811179", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94485, null, 0.101, null, 0.68314, null, 0.45711, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55663, "SRR10674418", "SRX7351695", "SRS5811178", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.", null, null, null, null, "Cntrol3", null, "isolate:biologocal replicate 18|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic responses of Bisphenol S", "bps050118", "bps050118", "An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "Cntrol3_1.fq.gz Cntrol3_2.fq.gz", "fastq fastq", 6742983200.0, 67429832.0, "Cntrol3 1.fq.gz", "0:100 1:100", "A:1801392073;C:1577630219;G:1545614005;T:1817857809;N:489094", 100, 100, null, null, 1801392073, 1577630219, 1545614005, 1817857809, 489094, "SRX7351695", "SRS5811178", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94386, null, 0.10779, null, 0.68832, null, 0.45545, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55664, "SRR10674419", "SRX7351694", "SRS5811177", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. 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The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "Cntrol2_1.fq.gz Cntrol2_2.fq.gz", "fastq fastq", 6750661000.0, 67506610.0, "Cntrol2 1.fq.gz", "0:100 1:100", "A:1796606666;C:1585909518;G:1556014239;T:1811284557;N:846020", 100, 100, null, null, 1796606666, 1585909518, 1556014239, 1811284557, 846020, "SRX7351694", "SRS5811177", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94397, null, 0.10007, null, 0.68708, null, 0.47779, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55665, "SRR10674420", "SRX7351693", "SRS5811174", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. 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The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP237283", null, null, "Cntrol1_1.fq.gz Cntrol1_2.fq.gz", "fastq fastq", 6766663000.0, 67666630.0, "Cntrol1 1.fq.gz", "0:100 1:100", "A:1825736389;C:1564390057;G:1532835305;T:1842876742;N:824507", 100, 100, null, null, 1825736389, 1564390057, 1532835305, 1842876742, 824507, "SRX7351693", "SRS5811174", "SRA1010884", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.94047, null, 0.12338, null, 0.68893, null, 0.46407, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-12-12", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [55666, "SRR10674421", "SRX7351692", "SRS5811176", "SRP237283", "PRJNA595113", "Transcriptomic responses of Bisphenol S on zebrafish", "PRJNA595113", "Other", "To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. 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